Dear All and Justin,
Suppose my protein complex contain 4 ADP, each ADP was in one subunit.
Suppose we use ATB to create the ligand ADP files for md. It seems the
situation is, regardless of which of the 4 ADP pdb files was submitted, ATB
will only give one identical set of topology files for ADP, and it cannot
distinguish from which ADP ligand ATB got the topology files for all 4
ADPs.
Here it lead to the question, how does GROMCS knows the position of each
ADP in the protein complex during the md process?
Let us think the question from another view. We have a protein-ligand
complex pdb, and the complex contains 1 subunit and 1 ligand. We got the
protein topology file by pdb2gmx, and we will find in the gro file the
value of the coordinates have been changed from the original pdb
coordinates for the protein-ligand. The same is true for the ligand, and if
we use prodrug to get the topology file for the ligand, we will find the
coordinate values of the ligand have been changed in comparison with that
in the ligand pdb from the protein-ligand pdb.
Thus, I would like to ask, after we edited the gro files by combining the
protein part coordinates and ligand part coordinates, how GROMCS keeps that
once the compiled gro file was transformed back to pdb, the ligands were in
the correct ligand binding pocket in the protein?
I am looking forward to getting the reply from you.
Brett
At 2016-04-19 20:13:03, "Justin Lemkul" <jalem...@vt.edu> wrote:
On 4/19/16 8:10 AM, Brett wrote:
Dear All,
It seems the external servers preparing the ligand files (antechamber
for example) not only optimize the coordinates of the ligands, but it
changes the ligand from one place to another place, thus the ligand
coordinates by the external server cannot occupy the ligand binding pocket
in the original protein-ligand complex.
I am looking forward to getting a reply from you on how to have the
external server processed ligand find the ligand binding pocket in the
protein-ligand complex for md.
Topology-generating servers aren't going to "find the ligand binding
pocket" -
your job is to make sure the original coordinates are preserved, as the
previous
message has instructed you on how to do.
-Justin
Brett
At 2016-04-19 19:44:23, "suniba" <sun.i...@gmail.com> wrote:
After pdb2gmx, protein topology is prepared. You prepare the ligand
topology from an external server or parametrize it. Then you prepare
complex.gro and include the ligand topology manually in topol.top (topology
generated by pdb2gmx). And for your second question, I used ATB today and
realized that one should always use "original geometry" co-ordinates as
'optimized geometry' will/may cause clashes with protein etc.. So, avoid
PRODRG server and use ATB and then download the co-ordinates and .itp of
original geometry. Rest process is same as mentioned in tutorial.
Regards
Sent from my iPhone
On 19-Apr-2016, at 4:58 pm, Brett <brettliu...@163.com> wrote:
Dear All,
I am learning the md of protein-ligand based on the Justin on-line
tutorial. My first question is, for the topology files we need to produce
the protein part and ligand part separately, and the input for pdb2gmx did
not contain the ligand part. After I got the ligand files, I find the
coordinate of the ligands was different from the ligand pdb in the
protein-complex pdb (although the rmsd between the ligand topology and the
ligand in the complex was 0). Then during md process how does GROMCS know
where is the position of the ligand in the complex?
Correspondingly, my second question is, suppose I have a protein
dimer with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was
apo. Then during the md process how does GROMACS know which subunit binding
with the cAMP and which subunit was apo?
I am looking forward to getting a reply from you.
Brett
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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